Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman. 1990.
“Basic Local Alignment Search Tool.” Journal of Molecular Biology 215 (3): 403–10.
https://doi.org/10.1016/S0022-2836(05)80360-2.
Engelhardt, B. E., M. I. Jordan, K. E. Muratore, and S. E. Brenner. 2005.
“Protein Molecular Function Prediction by Bayesian Phylogenomics.” PLOS Computational Biology 1 (5).
https://doi.org/10.1371/journal.pcbi.0010045.
Engelhardt, B. E., M. I. Jordan, J. R. Srouji, and S. E. Brenner. 2011.
“Genome-Scale Phylogenetic Function Annotation of Large and Diverse Protein Families.” Genome Research 21 (11): 1969–80.
https://doi.org/10.1101/gr.104687.109.
Gligorijević, Vladimir, P. Douglas Renfrew, Tomasz Kosciolek, Julia Koehler Leman, Daniel Berenberg, Tommi Vatanen, Chris Chandler, et al. 2021.
“Structure-Based Protein Function Prediction Using Graph Convolutional Networks.” Nature Communications 12 (1): 3168.
https://doi.org/10.1038/s41467-021-23303-9.
Jain, Aashish, and Daisuke Kihara. 2019.
“Phylo-PFP: Improved Automated Protein Function Prediction Using Phylogenetic Distance of Distantly Related Sequences.” Bioinformatics 35 (March): 753–59.
https://doi.org/10.1093/bioinformatics/bty704.
Kulmanov, Maxat, and Robert Hoehndorf. 2019.
“DeepGOPlus: Improved Protein Function Prediction from Sequence.” Edited by Lenore Cowen.
Bioinformatics, July, btz595.
https://doi.org/10.1093/bioinformatics/btz595.
Vega Yon, G. G., D. C. Thomas, J. Morrison, H. Mi, P. D. Thomas, and P. Marjoram. 2021.
“Bayesian Parameter Estimation for Automatic Annotation of Gene Functions Using Observational Data and Phylogenetic Trees.” PLoS Comput Biol 17: e1007948.
https://doi.org/10.1371/journal.pcbi.1007948.
Vega Yon, George G., Mary Jo Pugh, and Thomas W. Valente. 2022.
“Discrete Exponential-Family Models for Multivariate Binary Outcomes.” arXiv.
https://arxiv.org/abs/2211.00627.
You, Ronghui, Zihan Zhang, Yi Xiong, Fengzhu Sun, Hiroshi Mamitsuka, and Shanfeng Zhu. 2018.
“GOLabeler: Improving Sequence-Based Large-Scale Protein Function Prediction by Learning to Rank.” Edited by Jonathan Wren.
Bioinformatics 34 (14): 2465–73.
https://doi.org/10.1093/bioinformatics/bty130.
Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman. 1990.
“Basic Local Alignment Search Tool.” Journal of Molecular Biology 215 (3): 403–10.
https://doi.org/10.1016/S0022-2836(05)80360-2.
Engelhardt, B. E., M. I. Jordan, K. E. Muratore, and S. E. Brenner. 2005.
“Protein Molecular Function Prediction by Bayesian Phylogenomics.” PLOS Computational Biology 1 (5).
https://doi.org/10.1371/journal.pcbi.0010045.
Engelhardt, B. E., M. I. Jordan, J. R. Srouji, and S. E. Brenner. 2011.
“Genome-Scale Phylogenetic Function Annotation of Large and Diverse Protein Families.” Genome Research 21 (11): 1969–80.
https://doi.org/10.1101/gr.104687.109.
Gligorijević, Vladimir, P. Douglas Renfrew, Tomasz Kosciolek, Julia Koehler Leman, Daniel Berenberg, Tommi Vatanen, Chris Chandler, et al. 2021.
“Structure-Based Protein Function Prediction Using Graph Convolutional Networks.” Nature Communications 12 (1): 3168.
https://doi.org/10.1038/s41467-021-23303-9.
Jain, Aashish, and Daisuke Kihara. 2019.
“Phylo-PFP: Improved Automated Protein Function Prediction Using Phylogenetic Distance of Distantly Related Sequences.” Bioinformatics 35 (March): 753–59.
https://doi.org/10.1093/bioinformatics/bty704.
Kulmanov, Maxat, and Robert Hoehndorf. 2019.
“DeepGOPlus: Improved Protein Function Prediction from Sequence.” Edited by Lenore Cowen.
Bioinformatics, July, btz595.
https://doi.org/10.1093/bioinformatics/btz595.
Vega Yon, G. G., D. C. Thomas, J. Morrison, H. Mi, P. D. Thomas, and P. Marjoram. 2021.
“Bayesian Parameter Estimation for Automatic Annotation of Gene Functions Using Observational Data and Phylogenetic Trees.” PLoS Comput Biol 17: e1007948.
https://doi.org/10.1371/journal.pcbi.1007948.
Vega Yon, George G., Mary Jo Pugh, and Thomas W. Valente. 2022.
“Discrete Exponential-Family Models for Multivariate Binary Outcomes.” arXiv.
https://arxiv.org/abs/2211.00627.
You, Ronghui, Zihan Zhang, Yi Xiong, Fengzhu Sun, Hiroshi Mamitsuka, and Shanfeng Zhu. 2018.
“GOLabeler: Improving Sequence-Based Large-Scale Protein Function Prediction by Learning to Rank.” Edited by Jonathan Wren.
Bioinformatics 34 (14): 2465–73.
https://doi.org/10.1093/bioinformatics/bty130.